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For: Peres da Silva R, Suphavilai C, Nagarajan N. TUGDA: task uncertainty guided domain adaptation for robust generalization of cancer drug response prediction from in vitro to in vivo settings. Bioinformatics 2021;37:i76-i83. [PMID: 34000002 PMCID: PMC8275325 DOI: 10.1093/bioinformatics/btab299] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/27/2021] [Indexed: 11/21/2022]  Open
Number Cited by Other Article(s)
1
Dai W, Chen G, Peng W, Chen C, Fu X, Liu L, Liu L, Yu N. Domain alignment method based on masked variational autoencoder for predicting patient anticancer drug response. Methods 2025;238:61-73. [PMID: 40090506 DOI: 10.1016/j.ymeth.2025.03.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2024] [Revised: 02/03/2025] [Accepted: 03/14/2025] [Indexed: 03/18/2025]  Open
2
Jayagopal A, Walsh RJ, Hariprasannan KK, Mariappan R, Mahapatra D, Jaynes PW, Lim D, Peng Tan DS, Tan TZ, Pitt JJ, Jeyasekharan AD, Rajan V. A multi-task domain-adapted model to predict chemotherapy response from mutations in recurrently altered cancer genes. iScience 2025;28:111992. [PMID: 40160429 PMCID: PMC11952854 DOI: 10.1016/j.isci.2025.111992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 08/23/2024] [Accepted: 02/06/2025] [Indexed: 04/02/2025]  Open
3
Peng W, Chen C, Dai W, Yu N, Wang J. Predicting Clinical Anticancer Drug Response of Patients by Using Domain Alignment and Prototypical Learning. IEEE J Biomed Health Inform 2025;29:1534-1545. [PMID: 39292588 DOI: 10.1109/jbhi.2024.3462811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/20/2024]
4
Nguyen T, Campbell A, Kumar A, Amponsah E, Fiterau M, Shahriyari L. Optimal fusion of genotype and drug embeddings in predicting cancer drug response. Brief Bioinform 2024;25:bbae227. [PMID: 38754407 PMCID: PMC11097979 DOI: 10.1093/bib/bbae227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 04/14/2024] [Accepted: 04/25/2024] [Indexed: 05/18/2024]  Open
5
Kim J, Park SH, Lee H. PANCDR: precise medicine prediction using an adversarial network for cancer drug response. Brief Bioinform 2024;25:bbae088. [PMID: 38487849 PMCID: PMC10940842 DOI: 10.1093/bib/bbae088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 01/09/2024] [Accepted: 02/16/2024] [Indexed: 03/18/2024]  Open
6
Yuan S, Chen YC, Tsai CH, Chen HW, Shieh GS. Feature selection translates drug response predictors from cell lines to patients. Front Genet 2023;14:1217414. [PMID: 37519889 PMCID: PMC10382684 DOI: 10.3389/fgene.2023.1217414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 06/26/2023] [Indexed: 08/01/2023]  Open
7
Partin A, Brettin TS, Zhu Y, Narykov O, Clyde A, Overbeek J, Stevens RL. Deep learning methods for drug response prediction in cancer: Predominant and emerging trends. Front Med (Lausanne) 2023;10:1086097. [PMID: 36873878 PMCID: PMC9975164 DOI: 10.3389/fmed.2023.1086097] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 01/23/2023] [Indexed: 02/17/2023]  Open
8
Shen B, Feng F, Li K, Lin P, Ma L, Li H. A systematic assessment of deep learning methods for drug response prediction: from in vitro to clinical applications. Brief Bioinform 2023;24:6961794. [PMID: 36575826 DOI: 10.1093/bib/bbac605] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 10/30/2022] [Accepted: 12/09/2022] [Indexed: 12/29/2022]  Open
9
Yingtaweesittikul H, Wu J, Mongia A, Peres R, Ko K, Nagarajan N, Suphavilai C. CREAMMIST: an integrative probabilistic database for cancer drug response prediction. Nucleic Acids Res 2022;51:D1242-D1248. [PMID: 36259664 PMCID: PMC9825458 DOI: 10.1093/nar/gkac911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 09/18/2022] [Accepted: 10/11/2022] [Indexed: 01/30/2023]  Open
10
Ogunleye AZ, Piyawajanusorn C, Gonçalves A, Ghislat G, Ballester PJ. Interpretable Machine Learning Models to Predict the Resistance of Breast Cancer Patients to Doxorubicin from Their microRNA Profiles. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022;9:e2201501. [PMID: 35785523 PMCID: PMC9403644 DOI: 10.1002/advs.202201501] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 06/02/2022] [Indexed: 05/05/2023]
11
Out-of-distribution generalization from labelled and unlabelled gene expression data for drug response prediction. NAT MACH INTELL 2021. [DOI: 10.1038/s42256-021-00408-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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